2007-09-28 07:25:52 +08:00
|
|
|
<HEAD>
|
|
|
|
|
<TITLE>LAMMPS Users Manual</TITLE>
|
|
|
|
|
<META NAME="docnumber" CONTENT="Large-scale Atomic/Molecular Massively Parallel Simulator">
|
|
|
|
|
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
|
|
|
|
|
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
|
|
|
|
|
</HEAD>
|
|
|
|
|
|
|
|
|
|
<BODY>
|
|
|
|
|
|
2006-09-22 00:22:34 +08:00
|
|
|
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
|
|
|
|
|
|
|
|
|
:link(lws,http://lammps.sandia.gov)
|
|
|
|
|
:link(ld,Manual.html)
|
|
|
|
|
:link(lc,Section_commands.html#comm)
|
|
|
|
|
|
|
|
|
|
:line
|
|
|
|
|
|
|
|
|
|
<H1></H1>
|
|
|
|
|
|
|
|
|
|
LAMMPS Documentation :c,h3
|
|
|
|
|
|
2011-02-08 07:59:23 +08:00
|
|
|
Version info: :h4
|
2010-09-07 04:22:15 +08:00
|
|
|
|
2011-02-08 07:54:38 +08:00
|
|
|
The LAMMPS "version" is the date when it was released, such as 1 May
|
|
|
|
|
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
|
|
|
|
|
feature, we release it immediately, and post a notice on "this page of
|
|
|
|
|
the WWW site"_bug. Each dated copy of LAMMPS contains all the
|
|
|
|
|
features and bug-fixes up to and including that version date. The
|
|
|
|
|
version date is printed to the screen and logfile every time you run
|
|
|
|
|
LAMMPS. It is also in the file src/version.h and in the LAMMPS
|
|
|
|
|
directory name created when you unpack a tarball.
|
|
|
|
|
|
|
|
|
|
If you browse the HTML doc pages on the LAMMPS WWW site, they always
|
|
|
|
|
describe the most current version of LAMMPS. :ulb,l
|
|
|
|
|
|
|
|
|
|
If you browse the HTML doc pages included in your tarball, they
|
|
|
|
|
describe the version you have. :l
|
|
|
|
|
|
|
|
|
|
The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated
|
2011-05-28 07:59:19 +08:00
|
|
|
about once per month. This is because it is large, and we don't want
|
2011-08-24 07:10:45 +08:00
|
|
|
it to be part of very patch. :l
|
|
|
|
|
|
|
|
|
|
There is also a Developers.pdf file in the doc directory, which
|
|
|
|
|
describes the internal structure and algorithms of LAMMPS. :ule,l
|
2006-09-22 00:22:34 +08:00
|
|
|
|
|
|
|
|
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
|
|
|
|
|
Simulator.
|
|
|
|
|
|
|
|
|
|
LAMMPS is a classical molecular dynamics simulation code designed to
|
|
|
|
|
run efficiently on parallel computers. It was developed at Sandia
|
|
|
|
|
National Laboratories, a US Department of Energy facility, with
|
|
|
|
|
funding from the DOE. It is an open-source code, distributed freely
|
|
|
|
|
under the terms of the GNU Public License (GPL).
|
|
|
|
|
|
2011-02-08 07:54:38 +08:00
|
|
|
The primary developers of LAMMPS are "Steve Plimpton"_sjp, Aidan
|
|
|
|
|
Thompson, and Paul Crozier who can be contacted at
|
|
|
|
|
sjplimp,athomps,pscrozi at sandia.gov. The "LAMMPS WWW Site"_lws at
|
2010-01-15 07:50:34 +08:00
|
|
|
http://lammps.sandia.gov has more information about the code and its
|
|
|
|
|
uses.
|
2006-09-22 00:22:34 +08:00
|
|
|
|
2010-09-07 04:22:15 +08:00
|
|
|
:link(bug,http://lammps.sandia.gov/bug.html)
|
2010-05-07 23:11:21 +08:00
|
|
|
:link(sjp,http://www.sandia.gov/~sjplimp)
|
2006-09-22 00:22:34 +08:00
|
|
|
|
|
|
|
|
:line
|
|
|
|
|
|
|
|
|
|
The LAMMPS documentation is organized into the following sections. If
|
|
|
|
|
you find errors or omissions in this manual or have suggestions for
|
2006-09-26 23:30:56 +08:00
|
|
|
useful information to add, please send an email to the developers so
|
|
|
|
|
we can improve the LAMMPS documentation.
|
2006-09-22 00:22:34 +08:00
|
|
|
|
2007-06-26 08:03:39 +08:00
|
|
|
Once you are familiar with LAMMPS, you may want to bookmark "this
|
|
|
|
|
page"_Section_commands.html#comm at Section_commands.html#comm since
|
|
|
|
|
it gives quick access to documentation for all LAMMPS commands.
|
|
|
|
|
|
2006-09-22 00:22:34 +08:00
|
|
|
"PDF file"_Manual.pdf of the entire manual, generated by
|
|
|
|
|
"htmldoc"_http://www.easysw.com/htmldoc
|
|
|
|
|
|
|
|
|
|
"Introduction"_Section_intro.html :olb,l
|
|
|
|
|
1.1 "What is LAMMPS"_1_1 :ulb,b
|
|
|
|
|
1.2 "LAMMPS features"_1_2 :b
|
|
|
|
|
1.3 "LAMMPS non-features"_1_3 :b
|
|
|
|
|
1.4 "Open source distribution"_1_4 :b
|
|
|
|
|
1.5 "Acknowledgments and citations"_1_5 :ule,b
|
|
|
|
|
"Getting started"_Section_start.html :l
|
|
|
|
|
2.1 "What's in the LAMMPS distribution"_2_1 :ulb,b
|
|
|
|
|
2.2 "Making LAMMPS"_2_2 :b
|
2007-02-17 05:06:13 +08:00
|
|
|
2.3 "Making LAMMPS with optional packages"_2_3 :b
|
|
|
|
|
2.4 "Building LAMMPS as a library"_2_4 :b
|
2007-02-10 05:37:30 +08:00
|
|
|
2.5 "Running LAMMPS"_2_5 :b
|
|
|
|
|
2.6 "Command-line options"_2_6 :b
|
|
|
|
|
2.7 "Screen output"_2_7 :b
|
2011-05-27 07:45:23 +08:00
|
|
|
2.8 "Tips for users of previous versions"_2_8 :ule,b
|
2006-09-22 00:22:34 +08:00
|
|
|
"Commands"_Section_commands.html :l
|
|
|
|
|
3.1 "LAMMPS input script"_3_1 :ulb,b
|
|
|
|
|
3.2 "Parsing rules"_3_2 :b
|
|
|
|
|
3.3 "Input script structure"_3_3 :b
|
|
|
|
|
3.4 "Commands listed by category"_3_4 :b
|
|
|
|
|
3.5 "Commands listed alphabetically"_3_5 :ule,b
|
|
|
|
|
"How-to discussions"_Section_howto.html :l
|
|
|
|
|
4.1 "Restarting a simulation"_4_1 :ulb,b
|
|
|
|
|
4.2 "2d simulations"_4_2 :b
|
|
|
|
|
4.3 "CHARMM and AMBER force fields"_4_3 :b
|
|
|
|
|
4.4 "Running multiple simulations from one input script"_4_4 :b
|
2010-10-01 04:38:58 +08:00
|
|
|
4.5 "Multi-replica simulations"_4_5 :b
|
2006-09-22 00:22:34 +08:00
|
|
|
4.6 "Granular models"_4_6 :b
|
|
|
|
|
4.7 "TIP3P water model"_4_7 :b
|
|
|
|
|
4.8 "TIP4P water model"_4_8 :b
|
|
|
|
|
4.9 "SPC water model"_4_9 :b
|
2007-05-24 22:22:05 +08:00
|
|
|
4.10 "Coupling LAMMPS to other codes"_4_10 :b
|
2007-06-26 08:03:39 +08:00
|
|
|
4.11 "Visualizing LAMMPS snapshots"_4_11 :b
|
2010-10-15 07:23:43 +08:00
|
|
|
4.12 "Triclinic (non-orthogonal) simulation boxes"_4_12 :b
|
2007-06-26 08:03:39 +08:00
|
|
|
4.13 "NEMD simulations"_4_13 :b
|
2008-06-25 01:27:41 +08:00
|
|
|
4.14 "Extended spherical and aspherical particles"_4_14 :b
|
2009-01-27 04:14:19 +08:00
|
|
|
4.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_4_15 :b
|
2010-01-12 05:56:27 +08:00
|
|
|
4.16 "Thermostatting, barostatting, and compute temperature"_4_16 :b
|
2010-05-14 23:10:38 +08:00
|
|
|
4.17 "Walls"_4_17 :b
|
2010-11-02 23:05:51 +08:00
|
|
|
4.18 "Elastic constants"_4_18 :b
|
2011-01-04 00:42:55 +08:00
|
|
|
4.19 "Library interface to LAMMPS"_4_19 :b
|
|
|
|
|
4.20 "Calculating thermal conductivity"_4_20 :b
|
|
|
|
|
4.21 "Calculating viscosity"_4_21 :ule,b
|
2006-09-22 00:22:34 +08:00
|
|
|
"Example problems"_Section_example.html :l
|
|
|
|
|
"Performance & scalability"_Section_perf.html :l
|
|
|
|
|
"Additional tools"_Section_tools.html :l
|
2011-05-27 07:45:23 +08:00
|
|
|
"Modifying & extending LAMMPS"_Section_modify.html :l
|
2010-11-02 23:05:51 +08:00
|
|
|
"Python interface"_Section_python.html :l
|
|
|
|
|
9.1 "Extending Python with a serial version of LAMMPS"_9_1 :ulb,b
|
|
|
|
|
9.2 "Creating a shared MPI library"_9_2 :b
|
|
|
|
|
9.3 "Extending Python with a parallel version of LAMMPS"_9_3 :b
|
|
|
|
|
9.4 "Extending Python with MPI"_9_4 :b
|
|
|
|
|
9.5 "Testing the Python-LAMMPS interface"_9_5 :b
|
|
|
|
|
9.6 "Using LAMMPS from Python"_9_6 :b
|
|
|
|
|
9.7 "Example Python scripts that use LAMMPS"_9_7 :ule,b
|
2011-08-12 22:08:25 +08:00
|
|
|
"Using accelerated CPU and GPU styles"_Section_accelerate.html :l
|
2011-05-27 07:45:23 +08:00
|
|
|
10.1 "OPT package"_10_1 :ulb,b
|
|
|
|
|
10.2 "GPU package"_10_2 :b
|
|
|
|
|
10.3 "USER-CUDA package"_10_3 :b
|
|
|
|
|
10.4 "Comparison of GPU and USER-CUDA packages"_10_4 :ule,b
|
2006-09-22 00:22:34 +08:00
|
|
|
"Errors"_Section_errors.html :l
|
2011-05-27 07:45:23 +08:00
|
|
|
11.1 "Common problems"_11_1 :ulb,b
|
|
|
|
|
11.2 "Reporting bugs"_11_2 :b
|
|
|
|
|
11.3 "Error & warning messages"_11_3 :ule,b
|
2006-09-22 00:22:34 +08:00
|
|
|
"Future and history"_Section_history.html :l
|
2011-05-27 07:45:23 +08:00
|
|
|
12.1 "Coming attractions"_12_1 :ulb,b
|
|
|
|
|
12.2 "Past versions"_12_2 :ule,b
|
2006-09-22 00:22:34 +08:00
|
|
|
:ole
|
|
|
|
|
|
|
|
|
|
:link(1_1,Section_intro.html#1_1)
|
|
|
|
|
:link(1_2,Section_intro.html#1_2)
|
|
|
|
|
:link(1_3,Section_intro.html#1_3)
|
|
|
|
|
:link(1_4,Section_intro.html#1_4)
|
|
|
|
|
:link(1_5,Section_intro.html#1_5)
|
|
|
|
|
|
|
|
|
|
:link(2_1,Section_start.html#2_1)
|
|
|
|
|
:link(2_2,Section_start.html#2_2)
|
|
|
|
|
:link(2_3,Section_start.html#2_3)
|
|
|
|
|
:link(2_4,Section_start.html#2_4)
|
|
|
|
|
:link(2_5,Section_start.html#2_5)
|
|
|
|
|
:link(2_6,Section_start.html#2_6)
|
2007-02-10 05:37:30 +08:00
|
|
|
:link(2_7,Section_start.html#2_7)
|
|
|
|
|
:link(2_8,Section_start.html#2_8)
|
2006-09-22 00:22:34 +08:00
|
|
|
|
|
|
|
|
:link(3_1,Section_commands.html#3_1)
|
|
|
|
|
:link(3_2,Section_commands.html#3_2)
|
|
|
|
|
:link(3_3,Section_commands.html#3_3)
|
|
|
|
|
:link(3_4,Section_commands.html#3_4)
|
|
|
|
|
:link(3_5,Section_commands.html#3_5)
|
|
|
|
|
|
|
|
|
|
:link(4_1,Section_howto.html#4_1)
|
|
|
|
|
:link(4_2,Section_howto.html#4_2)
|
|
|
|
|
:link(4_3,Section_howto.html#4_3)
|
|
|
|
|
:link(4_4,Section_howto.html#4_4)
|
|
|
|
|
:link(4_5,Section_howto.html#4_5)
|
|
|
|
|
:link(4_6,Section_howto.html#4_6)
|
|
|
|
|
:link(4_7,Section_howto.html#4_7)
|
|
|
|
|
:link(4_8,Section_howto.html#4_8)
|
|
|
|
|
:link(4_9,Section_howto.html#4_9)
|
|
|
|
|
:link(4_10,Section_howto.html#4_10)
|
2007-02-23 00:52:24 +08:00
|
|
|
:link(4_11,Section_howto.html#4_11)
|
2007-06-26 08:03:39 +08:00
|
|
|
:link(4_12,Section_howto.html#4_12)
|
|
|
|
|
:link(4_13,Section_howto.html#4_13)
|
|
|
|
|
:link(4_14,Section_howto.html#4_14)
|
2007-09-28 07:25:52 +08:00
|
|
|
:link(4_15,Section_howto.html#4_15)
|
2008-04-05 05:15:50 +08:00
|
|
|
:link(4_16,Section_howto.html#4_16)
|
2010-05-07 23:11:21 +08:00
|
|
|
:link(4_17,Section_howto.html#4_17)
|
2010-05-14 23:10:38 +08:00
|
|
|
:link(4_18,Section_howto.html#4_18)
|
2010-11-02 23:05:51 +08:00
|
|
|
:link(4_19,Section_howto.html#4_19)
|
2011-01-04 00:42:55 +08:00
|
|
|
:link(4_20,Section_howto.html#4_20)
|
|
|
|
|
:link(4_21,Section_howto.html#4_21)
|
2010-11-02 23:05:51 +08:00
|
|
|
|
|
|
|
|
:link(9_1,Section_python.html#9_1)
|
|
|
|
|
:link(9_2,Section_python.html#9_2)
|
|
|
|
|
:link(9_3,Section_python.html#9_3)
|
|
|
|
|
:link(9_4,Section_python.html#9_4)
|
|
|
|
|
:link(9_5,Section_python.html#9_5)
|
|
|
|
|
:link(9_6,Section_python.html#9_6)
|
|
|
|
|
:link(9_7,Section_python.html#9_7)
|
|
|
|
|
|
2011-08-12 22:08:25 +08:00
|
|
|
:link(10_1,Section_accelerate.html#10_1)
|
|
|
|
|
:link(10_2,Section_accelerate.html#10_2)
|
|
|
|
|
:link(10_3,Section_accelerate.html#10_3)
|
|
|
|
|
:link(10_4,Section_accelerate.html#10_4)
|
2010-11-02 23:05:51 +08:00
|
|
|
|
2011-05-27 07:45:23 +08:00
|
|
|
:link(11_1,Section_errors.html#11_1)
|
|
|
|
|
:link(11_2,Section_errors.html#11_2)
|
|
|
|
|
:link(11_3,Section_errors.html#11_3)
|
|
|
|
|
|
|
|
|
|
:link(12_1,Section_history.html#12_1)
|
|
|
|
|
:link(12_2,Section_history.html#12_2)
|
2007-09-28 07:25:52 +08:00
|
|
|
|
|
|
|
|
</BODY>
|
